X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothur.h;h=b4fc3ce1c41171c0cde75a83f6365e12873984bc;hp=32f4778a7c1ee19db25eeb4e1eafaf74fabcd617;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hpb=03fae12080951ea1d889da5187386abc236cc334

diff --git a/mothur.h b/mothur.h
index 32f4778..b4fc3ce 100644
--- a/mothur.h
+++ b/mothur.h
@@ -120,6 +120,52 @@ struct diffPair {
 		reverseProb = rp;
 	}
 };
+
+/**********************************************************/
+struct CommonHeader {
+	unsigned int magicNumber;
+	string version;
+	unsigned long long indexOffset;
+	unsigned int indexLength;
+	unsigned int numReads;
+	unsigned short headerLength;
+	unsigned short keyLength;
+	unsigned short numFlowsPerRead;
+	int flogramFormatCode;
+	string flowChars; //length depends on number flow reads
+	string keySequence; //length depends on key length
+	
+	CommonHeader(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; }
+	~CommonHeader() { }
+};
+/**********************************************************/
+struct Header {
+	unsigned short headerLength;
+	unsigned short nameLength;
+	unsigned int numBases;
+	unsigned short clipQualLeft;
+	unsigned short clipQualRight;
+	unsigned short clipAdapterLeft;
+	unsigned short clipAdapterRight;
+	string name; //length depends on nameLength
+	string timestamp;
+	string region;
+	string xy;
+	
+	Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
+	~Header() { }
+};
+/**********************************************************/
+struct seqRead {
+	vector<unsigned short> flowgram;
+	vector<unsigned int> flowIndex;
+	string bases;
+	vector<unsigned int> qualScores;
+	
+	seqRead() { }
+	~seqRead() { }
+};
+
 /***********************************************************************/
 struct PDistCell{
 	ull index;
@@ -164,6 +210,16 @@ struct distlinePair {
 	int end;
 	
 };
+/************************************************************/
+struct oligosPair {
+	string forward;
+	string reverse;
+	
+	oligosPair() { forward = ""; reverse = "";  }
+	oligosPair(string f, string r) : forward(f), reverse(r) {}
+	~oligosPair() {}
+};
+
 /************************************************************/
 struct seqPriorityNode {
 	int numIdentical;
@@ -196,7 +252,24 @@ inline bool compareIndexes(PDistCell left, PDistCell right){
 //********************************************************************************************************************
 inline bool compareSpearman(spearmanRank left, spearmanRank right){
 	return (left.score < right.score);	
-} 
+}
+//********************************************************************************************************************
+inline double max(double left, double right){
+    if (left > right) { return left; }
+    else { return right; }
+}
+//********************************************************************************************************************
+inline double max(int left, double right){
+    double value = left;
+    if (left > right) { return value; }
+    else { return right; }
+}
+//********************************************************************************************************************
+inline double max(double left, int right){
+    double value = right;
+    if (left > value) { return left; }
+    else { return value; }
+}
 //********************************************************************************************************************
 //sorts highest to lowest
 inline bool compareSeqPriorityNodes(seqPriorityNode left, seqPriorityNode right){